subject:"\[Mauve\-users\] Mauve contig mover"

Re: [Mauve-users] Mauve contig mover

2015-11-03 Thread Mark Mandel

Dear Xiangchen,

I don’t know whether you can specify the number of iterations, but I don’t 
think you need to. The process proceeds through new alignments for as long as 
it can, and intermediate results are generated and available for you to view, 
so you can always check earlier results. In my experience, the process 
sometimes takes very few iterations (2-3) and sometimes more than 20, depending 
on the number of contigs and what order/orientation they were in initially. 
This has no bearing on the quality of the final ordering. Links below to 
additional documentation.

From the paper - 
http://bioinformatics.oxfordjournals.org/content/25/16/2071.full
"Mauve assumes contigs are in the correct order when filtering matches, so as 
the order is optimized, alignment results change. Therefore, results are 
refined through iterative alignment until no further ordering is possible."

Darling Lab site - http://darlinglab.org/mauve/user-guide/reordering.html

Take care,
Mark

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On Nov 3, 2015, at 8:31 PM, 
lixiangche...@outlook.com wrote:

Hi,

Currently I am using "Mauve contig mover" to make an ordering of contig. I find 
only 15 alignments in the result. I think the final alignment should be the 
best.  I think the more the iterations is, the more accurate the reodering is. 
So can I change the default number of alignments in  the reordering process?

Best,

Xiangchen


lixiangche...@outlook.com
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[Mauve-users] Mauve contig mover

2015-11-03 Thread lixiangche...@outlook.com

Hi,

Currently I am using "Mauve contig mover" to make an ordering of contig. I find 
only 15 alignments in the result. I think the final alignment should be the 
best.  I think the more the iterations is, the more accurate the reodering is. 
So can I change the default number of alignments in  the reordering process?

Best,

Xiangchen



lixiangche...@outlook.com
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Re: [Mauve-users] mauve contig mover from the command line

2013-10-31 Thread Aaron Darling

Hi Silvia,

After thinking about this for a while I am beginning to suspect there
may be a problem with the input files. Would it be possible for you to
send me the input files off-list either via compressed e-mail attachment
or dropbox so I can test it?

Thanks,
-Aaron

On Mon, 2013-10-14 at 12:49 -0400, Silvia Argimon wrote:
 Dear Joseph and Aaron,
 Thank you for your messages. As Aaron mentioned my genomes are small
 (2-4 Mb) so that shouldn't be a problem (it certainly hasn't been a
 problem in the past).
 I had a look at the /var/folders/yk/ directory and the permissions
 appeared as rwxr-xr-x. To address potential permissions issues, I
 chmod 777 the directory and the temp folder
 tqjv_9nx61n56rjpvr5v7cbcgn in it, and all the subdirectories in
 that too. Then tried again, but got the same error.
 I also tried to run the same command with sudo, but again same error.
 
 
 $ java -Xmx500m
 -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar 
 org.gel.mauve.contigs.ContigOrderer -output batch 1_assembly_1_mcm -ref 
 LrGG.fasta -draft 8447_5__1_k90-contigs.fa ref file: 
 org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
  and Reorder Contigs,normal] shown OS name is: Mac OS X arch: x86_64 
 Executing: progressiveMauve 
 --output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
  --skip-refinement --weight=200 
 --output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree
  
 --backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone
  
 /Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/ali
 gnment1/LrGG.fasta 
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa
 Storing raw sequence at 
/var/folders/yk/tqjv_9nx61n56rjpvr5v7cbcgn/T/rawseq813.000 libc++abi.dylib: 
terminate called throwing an exception Exited with error code: 134 
 
 
 
 I also tried to run the same command with sudo, but again same error,
 though the raw sequenced seemed to have been directed to another
 location in this case.
 
 $ sudo java -Xmx500m
 -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.ja r 
 org.gel.mauve.contigs.ContigOrderer -output batch1_assembly_1_mcm -ref 
 LrGG.fasta -draft 8447_5__1_k90-contigs.fa Password: ref file: 
 org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
  and Reorder Contigs,normal] shown OS name is: Mac OS X arch: x86_64 
 Executing: progressiveMauve 
 --output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
  --skip-refinement --weight=200 
 --output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree
  
 --backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone
  
 /Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly
 _1_mcm/alignment1/LrGG.fasta 
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa
 Storing raw sequence at /tmp/rawseq773.000 libc++abi.dylib: terminate called 
throwing an exception Exited with error code: 134



-- 
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman



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Re: [Mauve-users] mauve contig mover from the command line

2013-10-14 Thread Silvia Argimon

Dear Joseph and Aaron,
Thank you for your messages. As Aaron mentioned my genomes are small (2-4
Mb) so that shouldn't be a problem (it certainly hasn't been a problem in
the past).
I had a look at the /var/folders/yk/ directory and the permissions appeared
as rwxr-xr-x. To address potential permissions issues, I chmod 777 the
directory and the temp folder tqjv_9nx61n56rjpvr5v7cbcgn in it, and
all the subdirectories in that too. Then tried again, but got the same
error.
I also tried to run the same command with sudo, but again same error.

$ java -Xmx500m -cp
/Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar
org.gel.mauve.contigs.ContigOrderer -output batch 1_assembly_1_mcm -ref
LrGG.fasta -draft 8447_5__1_k90-contigs.fa ref file:
org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
and Reorder Contigs,normal] shown OS name is: Mac OS X arch: x86_64
Executing: progressiveMauve
--output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
--skip-refinement --weight=200
--output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree
--backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/LrGG.fasta
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa
Storing raw sequence at
/var/folders/yk/tqjv_9nx61n56rjpvr5v7cbcgn/T/rawseq813.000
libc++abi.dylib: terminate called throwing an exception Exited with error
code: 134

I also tried to run the same command with sudo, but again same error,
though the raw sequenced seemed to have been directed to another location
in this case.
$ sudo java -Xmx500m -cp
/Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.ja r
org.gel.mauve.contigs.ContigOrderer -output batch1_assembly_1_mcm -ref
LrGG.fasta -draft 8447_5__1_k90-contigs.fa Password: ref file:
org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
and Reorder Contigs,normal] shown OS name is: Mac OS X arch: x86_64
Executing: progressiveMauve
--output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
--skip-refinement --weight=200
--output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree
--backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/LrGG.fasta
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa
Storing raw sequence at /tmp/rawseq773.000 libc++abi.dylib: terminate
called throwing an exception Exited with error code: 134

Any advice on what else I could try?
Thanks,
Silvia


On Fri, Oct 11, 2013 at 6:25 PM, Joseph Fass joseph.f...@gmail.com wrote:

 That same error code has appeared previously on this list for (at least in
 one case) alignment of large - e.g. mammalian - genomes. Are you ordering
 something large?

 ~Joe





 On Fri, Oct 11, 2013 at 8:49 AM, Silvia Argimon s...@nyu.edu wrote:

 Hello!
 I started running the mauve contig mover from the command line a few
 months ago. I recently changed my computer though, and it's not working on
 my new system. I'm currently running Mac OS X 10.8.4, and java version
 1.6.0_51 on a 3.2 Ghz Quad-Core Intel Xeon processor. Before I was
 running Mac OS X 10.6.8, and the same java version on an iMac.

 Here's the command and error I'm getting:

 $ java -Xmx500m -cp
 /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar
 org.gel.mauve.contig
 s.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft
 8447_5__1_k90-contigs.fa
 ref file:
 org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
 and Reorder Contigs,normal]
 shown
 OS name is: Mac OS X arch: x86_64
 Executing:
  progressiveMauve
 --output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
 --skip-refinement --weight=200
 --output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree

[Mauve-users] mauve contig mover from the command line

2013-10-11 Thread Silvia Argimon

Hello!
I started running the mauve contig mover from the command line a few months
ago. I recently changed my computer though, and it's not working on my new
system. I'm currently running Mac OS X 10.8.4, and java version 1.6.0_51
on a 3.2 Ghz Quad-Core Intel Xeon processor. Before I was running Mac OS X
10.6.8, and the same java version on an iMac.

Here's the command and error I'm getting:

$ java -Xmx500m -cp
/Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar
org.gel.mauve.contig
s.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft
8447_5__1_k90-contigs.fa
ref file:
org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
and Reorder Contigs,normal]
shown
OS name is: Mac OS X arch: x86_64
Executing:
progressiveMauve
--output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
--skip-refinement --weight=200
--output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree
--backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/LrGG.fasta
/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa
Storing raw sequence at
/var/folders/yk/tqjv_9nx61n56rjpvr5v7cbcgn/T/rawseq10787.000
libc++abi.dylib: terminate called throwing an exception
Exited with error code: 134

I get the same error when I run this from the GUI.

Is this because of the new OS? Should I download a new version of Mauve?
I'm running the same one as I transferred it from my old to my new system.
Thanks you,
Silvia
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Re: [Mauve-users] mauve contig mover from the command line

2013-10-11 Thread Aaron Darling

Hi Silvia,
The program appears to be terminating as its attempting to create a
temporary file to store a raw format version of your sequence. I
wonder if there are problems writing to the /var/folders/yk/...
directory, possibly due to permissions problems or a full disk. Disk
space and large file problems do indeed happen more frequently with very
large genomes as Joe noted, although your Lactobacillus genomes are
probably quite small compared to the mammalian genomes some people are
aligning.

Best,
-Aaron

On Fri, 2013-10-11 at 11:49 -0400, Silvia Argimon wrote:
Hello!
I started running the mauve contig mover from the command line a few
months ago. I recently changed my computer though, and it's not
working on my new system. I'm currently running Mac OS X 10.8.4, and
java version 1.6.0_51 on a 3.2 Ghz Quad-Core Intel Xeon processor.
Before I was running Mac OS X 10.6.8, and the same java version on an
iMac.

Here's the command and error I'm getting:

$ java -Xmx500m
-cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar
org.gel.mauve.contig
s.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft
8447_5__1_k90-contigs.fa
ref file:
org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align
and Reorder Contigs,normal]
shown
OS name is: Mac OS X arch: x86_64
Executing:
progressiveMauve
--output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1
--skip-refinement --weight=200
--output-guide-tree=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.guide_tree

--backbone-output=/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/alignment1.backbone

/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/LrGG.fasta

/Users/Silvia/Documents/Lactobacillus/G-Project/Genome_Comparisons/Lb_assemblies_82_oral/batch1_assembly_1_mcm/alignment1/8447_5__1_k90-contigs.fa

Storing raw sequence
at /var/folders/yk/tqjv_9nx61n56rjpvr5v7cbcgn/T/rawseq10787.000
libc++abi.dylib: terminate called throwing an exception
Exited with error code: 134

I get the same error when I run this from the GUI.

Is this because of the new OS? Should I download a new version of
Mauve? I'm running the same one as I transferred it from my old to my
new system.
Thanks you,
Silvia

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Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
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http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk
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--
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Associate Professor, ithree institute
University of Technology Sydney
Australia

http://darlinglab.org
twitter: @koadman

UTS CRICOS Provider Code: 00099F
DISCLAIMER: This email message and any accompanying attachments may contain
confidential information.
If you are not the intended recipient, do not read, use, disseminate,
distribute or copy this message or
attachments. If you have received this message in error, please notify the
sender immediately and delete
this message. Any views expressed in this message are those of the individual
sender, except where the
sender expressly, and with authority, states them to be the views of the
University of Technology Sydney.
Before opening any attachments, please check them for viruses and defects.

Think. Green. Do.

Please consider the environment before printing this email.

Re: [Mauve-users] Mauve contig mover

[Mauve-users] Mauve contig mover

Re: [Mauve-users] mauve contig mover from the command line

Re: [Mauve-users] mauve contig mover from the command line

[Mauve-users] mauve contig mover from the command line

Re: [Mauve-users] mauve contig mover from the command line

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